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<!DOCTYPE html>
<!-- START: inst/pkgdown/templates/layout.html --><!-- Generated by pkgdown: do not edit by hand --><html lang="en" data-bs-theme="auto"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><title>The Unix Shell: Working With Files and Directories</title><meta name="viewport" content="width=device-width, initial-scale=1"><script src="assets/themetoggle.js"></script><link rel="stylesheet" type="text/css" href="assets/styles.css"><script src="assets/scripts.js" type="text/javascript"></script><!-- mathjax --><script type="text/x-mathjax-config">
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The Unix Shell
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<ul><li><a href="#creating-directories">Creating directories</a></li>
<li><a href="#moving-files-and-directories">Moving files and directories</a></li>
<li><a href="#copying-files-and-directories">Copying files and directories</a></li>
<li><a href="#removing-files-and-directories">Removing files and directories</a></li>
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<h1>Working With Files and Directories</h1>
<p>Last updated on 2024-03-08 |
<a href="https://github.com/swcarpentry/shell-novice/edit/main/episodes/03-create.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
<div class="text-end">
<button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
</div>
<div class="overview card">
<h2 class="card-header">Overview</h2>
<div class="row g-0">
<div class="col-md-4">
<div class="card-body">
<div class="inner">
<h3 class="card-title">Questions</h3>
<ul><li>How can I create, copy, and delete files and directories?</li>
<li>How can I edit files?</li>
</ul></div>
</div>
</div>
<div class="col-md-8">
<div class="card-body">
<div class="inner bordered">
<h3 class="card-title">Objectives</h3>
<ul><li>Create a directory hierarchy that matches a given diagram.</li>
<li>Create files in that hierarchy using an editor or by copying and
renaming existing files.</li>
<li>Delete, copy and move specified files and/or directories.</li>
</ul></div>
</div>
</div>
</div>
</div>
<section><h2 class="section-heading" id="creating-directories">Creating directories<a class="anchor" aria-label="anchor" href="#creating-directories"></a></h2>
<hr class="half-width"><p>We now know how to explore files and directories, but how do we
create them in the first place?</p>
<p>In this episode we will learn about creating and moving files and
directories, using the <code>exercise-data/writing</code> directory as
an example.</p>
<div class="section level3">
<h3 id="step-one-see-where-we-are-and-what-we-already-have">Step one: see where we are and what we already have<a class="anchor" aria-label="anchor" href="#step-one-see-where-we-are-and-what-we-already-have"></a></h3>
<p>We should still be in the <code>shell-lesson-data</code> directory on
the Desktop, which we can check using:</p>
<div class="codewrapper sourceCode" id="cb1">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">$</span> pwd</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>/Users/nelle/Desktop/shell-lesson-data</code></pre>
</div>
<p>Next we’ll move to the <code>exercise-data/writing</code> directory
and see what it contains:</p>
<div class="codewrapper sourceCode" id="cb3">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">$</span> cd exercise-data/writing/</span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a><span class="ex">$</span> ls <span class="at">-F</span></span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>haiku.txt LittleWomen.txt</code></pre>
</div>
</div>
<div class="section level3">
<h3 id="create-a-directory">Create a directory<a class="anchor" aria-label="anchor" href="#create-a-directory"></a></h3>
<p>Let’s create a new directory called <code>thesis</code> using the
command <code>mkdir thesis</code> (which has no output):</p>
<div class="codewrapper sourceCode" id="cb5">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="ex">$</span> mkdir thesis</span></code></pre>
</div>
<p>As you might guess from its name, <code>mkdir</code> means ‘make
directory’. Since <code>thesis</code> is a relative path (i.e., does not
have a leading slash, like <code>/what/ever/thesis</code>), the new
directory is created in the current working directory:</p>
<div class="codewrapper sourceCode" id="cb6">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="ex">$</span> ls <span class="at">-F</span></span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>haiku.txt LittleWomen.txt thesis/</code></pre>
</div>
<p>Since we’ve just created the <code>thesis</code> directory, there’s
nothing in it yet:</p>
<div class="codewrapper sourceCode" id="cb8">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="ex">$</span> ls <span class="at">-F</span> thesis</span></code></pre>
</div>
<p>Note that <code>mkdir</code> is not limited to creating single
directories one at a time. The <code>-p</code> option allows
<code>mkdir</code> to create a directory with nested subdirectories in a
single operation:</p>
<div class="codewrapper sourceCode" id="cb9">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="ex">$</span> mkdir <span class="at">-p</span> ../project/data ../project/results</span></code></pre>
</div>
<p>The <code>-R</code> option to the <code>ls</code> command will list
all nested subdirectories within a directory. Let’s use
<code>ls -FR</code> to recursively list the new directory hierarchy we
just created in the <code>project</code> directory:</p>
<div class="codewrapper sourceCode" id="cb10">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a><span class="ex">$</span> ls <span class="at">-FR</span> ../project</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>../project/:
data/ results/
../project/data:
../project/results:</code></pre>
</div>
<div id="two-ways-of-doing-the-same-thing" class="callout">
<div class="callout-square">
<i class="callout-icon" data-feather="bell"></i>
</div>
<div id="two-ways-of-doing-the-same-thing" class="callout-inner">
<h3 class="callout-title">Two ways of doing the same thing</h3>
<div class="callout-content">
<p>Using the shell to create a directory is no different than using a
file explorer. If you open the current directory using your operating
system’s graphical file explorer, the <code>thesis</code> directory will
appear there too. While the shell and the file explorer are two
different ways of interacting with the files, the files and directories
themselves are the same.</p>
</div>
</div>
</div>
<div id="good-names-for-files-and-directories" class="callout">
<div class="callout-square">
<i class="callout-icon" data-feather="bell"></i>
</div>
<div id="good-names-for-files-and-directories" class="callout-inner">
<h3 class="callout-title">Good names for files and directories</h3>
<div class="callout-content">
<p>Complicated names of files and directories can make your life painful
when working on the command line. Here we provide a few useful tips for
the names of your files and directories.</p>
<ol style="list-style-type: decimal"><li>Don’t use spaces.</li>
</ol><p>Spaces can make a name more meaningful, but since spaces are used to
separate arguments on the command line it is better to avoid them in
names of files and directories. You can use <code>-</code> or
<code>_</code> instead (e.g. <code>north-pacific-gyre/</code> rather
than <code>north pacific gyre/</code>). To test this out, try typing
<code>mkdir north pacific gyre</code> and see what directory (or
directories!) are made when you check with <code>ls -F</code>.</p>
<ol start="2" style="list-style-type: decimal"><li>Don’t begin the name with <code>-</code> (dash).</li>
</ol><p>Commands treat names starting with <code>-</code> as options.</p>
<ol start="3" style="list-style-type: decimal"><li>Stick with letters, numbers, <code>.</code> (period or ‘full stop’),
<code>-</code> (dash) and <code>_</code> (underscore).</li>
</ol><p>Many other characters have special meanings on the command line. We
will learn about some of these during this lesson. There are special
characters that can cause your command to not work as expected and can
even result in data loss.</p>
<p>If you need to refer to names of files or directories that have
spaces or other special characters, you should surround the name in
single <a href="https://www.gnu.org/software/bash/manual/html_node/Quoting.html" class="external-link">quotes</a>
(<code>''</code>).</p>
</div>
</div>
</div>
</div>
<div class="section level3">
<h3 id="create-a-text-file">Create a text file<a class="anchor" aria-label="anchor" href="#create-a-text-file"></a></h3>
<p>Let’s change our working directory to <code>thesis</code> using
<code>cd</code>, then run a text editor called Nano to create a file
called <code>draft.txt</code>:</p>
<div class="codewrapper sourceCode" id="cb12">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="ex">$</span> cd thesis</span>
<span id="cb12-2"><a href="#cb12-2" tabindex="-1"></a><span class="ex">$</span> nano draft.txt</span></code></pre>
</div>
<div id="which-editor" class="callout">
<div class="callout-square">
<i class="callout-icon" data-feather="bell"></i>
</div>
<div id="which-editor" class="callout-inner">
<h3 class="callout-title">Which Editor?</h3>
<div class="callout-content">
<p>When we say, ‘<code>nano</code> is a text editor’ we really do mean
‘text’. It can only work with plain character data, not tables, images,
or any other human-friendly media. We use it in examples because it is
one of the least complex text editors. However, because of this trait,
it may not be powerful enough or flexible enough for the work you need
to do after this workshop. On Unix systems (such as Linux and macOS),
many programmers use <a href="https://www.gnu.org/software/emacs/" class="external-link">Emacs</a> or <a href="https://www.vim.org/" class="external-link">Vim</a> (both of which require more time to
learn), or a graphical editor such as <a href="https://projects.gnome.org/gedit/" class="external-link">Gedit</a> or <a href="https://code.visualstudio.com/" class="external-link">VScode</a>. On Windows, you may
wish to use <a href="https://notepad-plus-plus.org/" class="external-link">Notepad++</a>.
Windows also has a built-in editor called <code>notepad</code> that can
be run from the command line in the same way as <code>nano</code> for
the purposes of this lesson.</p>
<p>No matter what editor you use, you will need to know where it
searches for and saves files. If you start it from the shell, it will
(probably) use your current working directory as its default location.
If you use your computer’s start menu, it may want to save files in your
Desktop or Documents directory instead. You can change this by
navigating to another directory the first time you ‘Save As…’</p>
</div>
</div>
</div>
<p>Let’s type in a few lines of text.</p>
<figure><img src="fig/nano-screenshot.png" alt="screenshot of nano text editor in action with the text It's not publish or perish any more, it's share and thrive" class="figure mx-auto d-block"></figure><p>Once we’re happy with our text, we can press
<kbd>Ctrl</kbd>+<kbd>O</kbd> (press the <kbd>Ctrl</kbd> or
<kbd>Control</kbd> key and, while holding it down, press the
<kbd>O</kbd> key) to write our data to disk. We will be asked to provide
a name for the file that will contain our text. Press <kbd>Return</kbd>
to accept the suggested default of <code>draft.txt</code>.</p>
<p>Once our file is saved, we can use <kbd>Ctrl</kbd>+<kbd>X</kbd> to
quit the editor and return to the shell.</p>
<div id="control-ctrl-or-key" class="callout">
<div class="callout-square">
<i class="callout-icon" data-feather="bell"></i>
</div>
<div id="control-ctrl-or-key" class="callout-inner">
<h3 class="callout-title">Control, Ctrl, or ^ Key</h3>
<div class="callout-content">
<p>The Control key is also called the ‘Ctrl’ key. There are various ways
in which using the Control key may be described. For example, you may
see an instruction to press the <kbd>Control</kbd> key and, while
holding it down, press the <kbd>X</kbd> key, described as any of:</p>
<ul><li><code>Control-X</code></li>
<li><code>Control+X</code></li>
<li><code>Ctrl-X</code></li>
<li><code>Ctrl+X</code></li>
<li><code>^X</code></li>
<li><code>C-x</code></li>
</ul><p>In nano, along the bottom of the screen you’ll see
<code>^G Get Help ^O WriteOut</code>. This means that you can use
<code>Control-G</code> to get help and <code>Control-O</code> to save
your file.</p>
</div>
</div>
</div>
<p><code>nano</code> doesn’t leave any output on the screen after it
exits, but <code>ls</code> now shows that we have created a file called
<code>draft.txt</code>:</p>
<div class="codewrapper sourceCode" id="cb13">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" tabindex="-1"></a><span class="ex">$</span> ls</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code><span><span class="va">draft.txt</span></span></code></pre>
</div>
<div id="creating-files-a-different-way" class="callout challenge">
<div class="callout-square">
<i class="callout-icon" data-feather="zap"></i>
</div>
<div id="creating-files-a-different-way" class="callout-inner">
<h3 class="callout-title">Creating Files a Different Way</h3>
<div class="callout-content">
<p>We have seen how to create text files using the <code>nano</code>
editor. Now, try the following command:</p>
<div class="codewrapper sourceCode" id="cb15">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb15-1"><a href="#cb15-1" tabindex="-1"></a><span class="ex">$</span> touch my_file.txt</span></code></pre>
</div>
<ol style="list-style-type: decimal"><li><p>What did the <code>touch</code> command do? When you look at your
current directory using the GUI file explorer, does the file show
up?</p></li>
<li><p>Use <code>ls -l</code> to inspect the files. How large is
<code>my_file.txt</code>?</p></li>
<li><p>When might you want to create a file this way?</p></li>
</ol></div>
</div>
</div>
<div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
<div class="accordion-item">
<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
<h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
</button>
<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
<div class="accordion-body">
<ol style="list-style-type: decimal"><li><p>The <code>touch</code> command generates a new file called
<code>my_file.txt</code> in your current directory. You can observe this
newly generated file by typing <code>ls</code> at the command line
prompt. <code>my_file.txt</code> can also be viewed in your GUI file
explorer.</p></li>
<li><p>When you inspect the file with <code>ls -l</code>, note that the
size of <code>my_file.txt</code> is 0 bytes. In other words, it contains
no data. If you open <code>my_file.txt</code> using your text editor it
is blank.</p></li>
<li><p>Some programs do not generate output files themselves, but
instead require that empty files have already been generated. When the
program is run, it searches for an existing file to populate with its
output. The touch command allows you to efficiently generate a blank
text file to be used by such programs.</p></li>
</ol></div>
</div>
</div>
</div>
<div id="creating-files-a-different-way" class="callout discussion">
<div class="callout-square">
<i class="callout-icon" data-feather="message-circle"></i>
</div>
<div id="creating-files-a-different-way" class="callout-inner">
<h3 class="callout-title">Creating Files a Different Way<em>
(continued)</em>
</h3>
<div class="callout-content">
<p>To avoid confusion later on, we suggest removing the file you’ve just
created before proceeding with the rest of the episode, otherwise future
outputs may vary from those given in the lesson. To do this, use the
following command:</p>
<div class="codewrapper sourceCode" id="cb16">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb16-1"><a href="#cb16-1" tabindex="-1"></a><span class="ex">$</span> rm my_file.txt</span></code></pre>
</div>
</div>
</div>
</div>
<div id="whats-in-a-name" class="callout">
<div class="callout-square">
<i class="callout-icon" data-feather="bell"></i>
</div>
<div id="whats-in-a-name" class="callout-inner">
<h3 class="callout-title">What’s In A Name?</h3>
<div class="callout-content">
<p>You may have noticed that all of Nelle’s files are named ‘something
dot something’, and in this part of the lesson, we always used the
extension <code>.txt</code>. This is just a convention; we can call a
file <code>mythesis</code> or almost anything else we want. However,
most people use two-part names most of the time to help them (and their
programs) tell different kinds of files apart. The second part of such a
name is called the <strong>filename extension</strong> and indicates
what type of data the file holds: <code>.txt</code> signals a plain text
file, <code>.pdf</code> indicates a PDF document, <code>.cfg</code> is a
configuration file full of parameters for some program or other,
<code>.png</code> is a PNG image, and so on.</p>
<p>This is just a convention, albeit an important one. Files merely
contain bytes; it’s up to us and our programs to interpret those bytes
according to the rules for plain text files, PDF documents,
configuration files, images, and so on.</p>
<p>Naming a PNG image of a whale as <code>whale.mp3</code> doesn’t
somehow magically turn it into a recording of whale song, though it
<em>might</em> cause the operating system to associate the file with a
music player program. In this case, if someone double-clicked
<code>whale.mp3</code> in a file explorer program, the music player will
automatically (and erroneously) attempt to open the
<code>whale.mp3</code> file.</p>
</div>
</div>
</div>
</div>
</section><section><h2 class="section-heading" id="moving-files-and-directories">Moving files and directories<a class="anchor" aria-label="anchor" href="#moving-files-and-directories"></a></h2>
<hr class="half-width"><p>Returning to the <code>shell-lesson-data/exercise-data/writing</code>
directory,</p>
<div class="codewrapper sourceCode" id="cb17">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb17-1"><a href="#cb17-1" tabindex="-1"></a><span class="ex">$</span> cd ~/Desktop/shell-lesson-data/exercise-data/writing</span></code></pre>
</div>
<p>In our <code>thesis</code> directory we have a file
<code>draft.txt</code> which isn’t a particularly informative name, so
let’s change the file’s name using <code>mv</code>, which is short for
‘move’:</p>
<div class="codewrapper sourceCode" id="cb18">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb18-1"><a href="#cb18-1" tabindex="-1"></a><span class="ex">$</span> mv thesis/draft.txt thesis/quotes.txt</span></code></pre>
</div>
<p>The first argument tells <code>mv</code> what we’re ‘moving’, while
the second is where it’s to go. In this case, we’re moving
<code>thesis/draft.txt</code> to <code>thesis/quotes.txt</code>, which
has the same effect as renaming the file. Sure enough, <code>ls</code>
shows us that <code>thesis</code> now contains one file called
<code>quotes.txt</code>:</p>
<div class="codewrapper sourceCode" id="cb19">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb19-1"><a href="#cb19-1" tabindex="-1"></a><span class="ex">$</span> ls thesis</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code><span><span class="va">quotes.txt</span></span></code></pre>
</div>
<p>One must be careful when specifying the target file name, since
<code>mv</code> will silently overwrite any existing file with the same
name, which could lead to data loss. By default, <code>mv</code> will
not ask for confirmation before overwriting files. However, an
additional option, <code>mv -i</code> (or
<code>mv --interactive</code>), will cause <code>mv</code> to request
such confirmation.</p>
<p>Note that <code>mv</code> also works on directories.</p>
<p>Let’s move <code>quotes.txt</code> into the current working
directory. We use <code>mv</code> once again, but this time we’ll use
just the name of a directory as the second argument to tell
<code>mv</code> that we want to keep the filename but put the file
somewhere new. (This is why the command is called ‘move’.) In this case,
the directory name we use is the special directory name <code>.</code>
that we mentioned earlier.</p>
<div class="codewrapper sourceCode" id="cb21">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1" tabindex="-1"></a><span class="ex">$</span> mv thesis/quotes.txt .</span></code></pre>
</div>
<p>The effect is to move the file from the directory it was in to the
current working directory. <code>ls</code> now shows us that
<code>thesis</code> is empty:</p>
<div class="codewrapper sourceCode" id="cb22">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb22-1"><a href="#cb22-1" tabindex="-1"></a><span class="ex">$</span> ls thesis</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>$</code></pre>
</div>
<p>Alternatively, we can confirm the file <code>quotes.txt</code> is no
longer present in the <code>thesis</code> directory by explicitly trying
to list it:</p>
<div class="codewrapper sourceCode" id="cb24">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb24-1"><a href="#cb24-1" tabindex="-1"></a><span class="ex">$</span> ls thesis/quotes.txt</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">ERROR<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="error" tabindex="0"><code>ls: cannot access 'thesis/quotes.txt': No such file or directory</code></pre>
</div>
<p><code>ls</code> with a filename or directory as an argument only
lists the requested file or directory. If the file given as the argument
doesn’t exist, the shell returns an error as we saw above. We can use
this to see that <code>quotes.txt</code> is now present in our current
directory:</p>
<div class="codewrapper sourceCode" id="cb26">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb26-1"><a href="#cb26-1" tabindex="-1"></a><span class="ex">$</span> ls quotes.txt</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code><span><span class="va">quotes.txt</span></span></code></pre>
</div>
<div id="moving-files-to-a-new-folder" class="callout challenge">
<div class="callout-square">
<i class="callout-icon" data-feather="zap"></i>
</div>
<div id="moving-files-to-a-new-folder" class="callout-inner">
<h3 class="callout-title">Moving Files to a new folder</h3>
<div class="callout-content">
<p>After running the following commands, Jamie realizes that she put the
files <code>sucrose.dat</code> and <code>maltose.dat</code> into the
wrong folder. The files should have been placed in the <code>raw</code>
folder.</p>
<div class="codewrapper sourceCode" id="cb28">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb28-1"><a href="#cb28-1" tabindex="-1"></a><span class="ex">$</span> ls <span class="at">-F</span></span>
<span id="cb28-2"><a href="#cb28-2" tabindex="-1"></a> <span class="ex">analyzed/</span> raw/</span>
<span id="cb28-3"><a href="#cb28-3" tabindex="-1"></a><span class="ex">$</span> ls <span class="at">-F</span> analyzed</span>
<span id="cb28-4"><a href="#cb28-4" tabindex="-1"></a><span class="ex">fructose.dat</span> glucose.dat maltose.dat sucrose.dat</span>
<span id="cb28-5"><a href="#cb28-5" tabindex="-1"></a><span class="ex">$</span> cd analyzed</span></code></pre>
</div>
<p>Fill in the blanks to move these files to the <code>raw/</code>
folder (i.e. the one she forgot to put them in)</p>
<div class="codewrapper sourceCode" id="cb29">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb29-1"><a href="#cb29-1" tabindex="-1"></a><span class="ex">$</span> mv sucrose.dat maltose.dat ____/____</span></code></pre>
</div>
</div>
</div>
</div>
<div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
<div class="accordion-item">
<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
<h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
</button>
<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
<div class="accordion-body">
<div class="codewrapper sourceCode" id="cb30">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb30-1"><a href="#cb30-1" tabindex="-1"></a><span class="ex">$</span> mv sucrose.dat maltose.dat ../raw</span></code></pre>
</div>
<p>Recall that <code>..</code> refers to the parent directory (i.e. one
above the current directory) and that <code>.</code> refers to the
current directory.</p>
</div>
</div>
</div>
</div>
</section><section><h2 class="section-heading" id="copying-files-and-directories">Copying files and directories<a class="anchor" aria-label="anchor" href="#copying-files-and-directories"></a></h2>
<hr class="half-width"><p>The <code>cp</code> command works very much like <code>mv</code>,
except it copies a file instead of moving it. We can check that it did
the right thing using <code>ls</code> with two paths as arguments — like
most Unix commands, <code>ls</code> can be given multiple paths at
once:</p>
<div class="codewrapper sourceCode" id="cb31">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb31-1"><a href="#cb31-1" tabindex="-1"></a><span class="ex">$</span> cp quotes.txt thesis/quotations.txt</span>
<span id="cb31-2"><a href="#cb31-2" tabindex="-1"></a><span class="ex">$</span> ls quotes.txt thesis/quotations.txt</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>quotes.txt thesis/quotations.txt</code></pre>
</div>
<p>We can also copy a directory and all its contents by using the <a href="https://en.wikipedia.org/wiki/Recursion" class="external-link">recursive</a> option
<code>-r</code>, e.g. to back up a directory:</p>
<div class="codewrapper sourceCode" id="cb33">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb33-1"><a href="#cb33-1" tabindex="-1"></a><span class="ex">$</span> cp <span class="at">-r</span> thesis thesis_backup</span></code></pre>
</div>
<p>We can check the result by listing the contents of both the
<code>thesis</code> and <code>thesis_backup</code> directory:</p>
<div class="codewrapper sourceCode" id="cb34">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb34-1"><a href="#cb34-1" tabindex="-1"></a><span class="ex">$</span> ls thesis thesis_backup</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code><span><span class="va">thesis</span><span class="op">:</span></span>
<span><span class="va">quotations.txt</span></span>
<span></span>
<span><span class="va">thesis_backup</span><span class="op">:</span></span>
<span><span class="va">quotations.txt</span></span></code></pre>
</div>
<p>It is important to include the <code>-r</code> flag. If you want to
copy a directory and you omit this option you will see a message that
the directory has been omitted because
<code>-r not specified</code>.</p>
<div class="codewrapper sourceCode" id="cb36">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb36-1"><a href="#cb36-1" tabindex="-1"></a><span class="ex">$</span> cp thesis thesis_backup</span>
<span id="cb36-2"><a href="#cb36-2" tabindex="-1"></a><span class="ex">cp:</span> <span class="at">-r</span> not specified<span class="kw">;</span> <span class="ex">omitting</span> directory <span class="st">'thesis'</span></span></code></pre>
</div>
<div id="renaming-files" class="callout challenge">
<div class="callout-square">
<i class="callout-icon" data-feather="zap"></i>
</div>
<div id="renaming-files" class="callout-inner">
<h3 class="callout-title">Renaming Files</h3>
<div class="callout-content">
<p>Suppose that you created a plain-text file in your current directory
to contain a list of the statistical tests you will need to do to
analyze your data, and named it <code>statstics.txt</code></p>
<p>After creating and saving this file you realize you misspelled the
filename! You want to correct the mistake, which of the following
commands could you use to do so?</p>
<ol style="list-style-type: decimal"><li><code>cp statstics.txt statistics.txt</code></li>
<li><code>mv statstics.txt statistics.txt</code></li>
<li><code>mv statstics.txt .</code></li>
<li><code>cp statstics.txt .</code></li>
</ol></div>
</div>
</div>
<div id="accordionSolution3" class="accordion challenge-accordion accordion-flush">
<div class="accordion-item">
<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
<h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
</button>
<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
<div class="accordion-body">
<ol style="list-style-type: decimal"><li>No. While this would create a file with the correct name, the
incorrectly named file still exists in the directory and would need to
be deleted.</li>
<li>Yes, this would work to rename the file.</li>
<li>No, the period(.) indicates where to move the file, but does not
provide a new file name; identical file names cannot be created.</li>
<li>No, the period(.) indicates where to copy the file, but does not
provide a new file name; identical file names cannot be created.</li>
</ol></div>
</div>
</div>
</div>
<div id="moving-and-copying" class="callout challenge">
<div class="callout-square">
<i class="callout-icon" data-feather="zap"></i>
</div>
<div id="moving-and-copying" class="callout-inner">
<h3 class="callout-title">Moving and Copying</h3>
<div class="callout-content">
<p>What is the output of the closing <code>ls</code> command in the
sequence shown below?</p>
<div class="codewrapper sourceCode" id="cb37">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb37-1"><a href="#cb37-1" tabindex="-1"></a><span class="ex">$</span> pwd</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code>/Users/jamie/data</code></pre>
</div>
<div class="codewrapper sourceCode" id="cb39">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb39-1"><a href="#cb39-1" tabindex="-1"></a><span class="ex">$</span> ls</span></code></pre>
</div>
<div class="codewrapper">
<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="output" tabindex="0"><code><span><span class="va">proteins.dat</span></span></code></pre>
</div>
<div class="codewrapper sourceCode" id="cb41">
<h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
</h3>
<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb41-1"><a href="#cb41-1" tabindex="-1"></a><span class="ex">$</span> mkdir recombined</span>
<span id="cb41-2"><a href="#cb41-2" tabindex="-1"></a><span class="ex">$</span> mv proteins.dat recombined/</span>
<span id="cb41-3"><a href="#cb41-3" tabindex="-1"></a><span class="ex">$</span> cp recombined/proteins.dat ../proteins-saved.dat</span>
<span id="cb41-4"><a href="#cb41-4" tabindex="-1"></a><span class="ex">$</span> ls</span></code></pre>
</div>
<ol style="list-style-type: decimal"><li><code>proteins-saved.dat recombined</code></li>
<li><code>recombined</code></li>
<li><code>proteins.dat recombined</code></li>
<li><code>proteins-saved.dat</code></li>
</ol></div>
</div>
</div>
<div id="accordionSolution4" class="accordion challenge-accordion accordion-flush">
<div class="accordion-item">
<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
<h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
</button>
<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
<div class="accordion-body">
<p>We start in the <code>/Users/jamie/data</code> directory, and create
a new folder called <code>recombined</code>. The second line moves
(<code>mv</code>) the file <code>proteins.dat</code> to the new folder
(<code>recombined</code>). The third line makes a copy of the file we
just moved. The tricky part here is where the file was copied to. Recall
that <code>..</code> means ‘go up a level’, so the copied file is now in
<code>/Users/jamie</code>. Notice that <code>..</code> is interpreted
with respect to the current working directory, <strong>not</strong> with
respect to the location of the file being copied. So, the only thing
that will show using ls (in <code>/Users/jamie/data</code>) is the
recombined folder.</p>
<ol style="list-style-type: decimal"><li>No, see explanation above. <code>proteins-saved.dat</code> is
located at <code>/Users/jamie</code>
</li>
<li>Yes</li>
<li>No, see explanation above. <code>proteins.dat</code> is located at
<code>/Users/jamie/data/recombined</code>
</li>
<li>No, see explanation above. <code>proteins-saved.dat</code> is